b3b3bib.sourceforge.net/help/b3.pdf · chapter 1: the b3 environment 1 1 the b3 environment ... you...

B3 Manual

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This is the manual of B3, version 0.4.

Copyright c© 2005-2009 Julien Dutheil, Christian Wiethol

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Table of Contents

1 The B3 Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.1 Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.2 Importing and file formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

1.2.1 The BibView window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.2.2 Scanning a directory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31.2.3 Fetching Pubmed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

1.3 Using external applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2 Extended functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62.1 The journal database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

2.1.1 The Journal Dictionary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62.1.2 Checking journal names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62.1.3 Switching between ’Full’ and ’Abbreviate’ modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

2.2 The author database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72.2.1 What is it for? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72.2.2 How does-it work? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72.2.3 Adding entries to the author database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

2.3 Searching a database (beta) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92.4 Using style-sheets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

3 Interacting with word processors . . . . . . . . . . . . . . . . . . . . . . . . . . . 113.1 Exporting to OpenOffice using a flat file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

3.1.1 Export to a Text/CSV file. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113.1.1.1 The Database Configuration Dialog window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113.1.1.2 Exporting a database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

3.1.2 Importing a Text/CSV file into OpenOffice. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123.1.2.1 Creating a new database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123.1.2.2 Setting up the bibliography database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133.1.2.3 You’re done :-) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

3.2 Exporting to OpenOffice using MySQL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153.3 Using LATEX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193.4 Processing OpenDocument texts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

3.4.1 Known issues and how to avoid them... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Chapter 1: The B3 Environment 1

1 The B3 Environment

When you launch B3, you have a void desktop with a menu bar. Some features are not availablesince no database is open. However you may configure a few things if you want. To open aexisting database, click on the File menu, Read item. To create a new database, click on theFile menu, New item.

Figure 1.1: The B3 environment. No database is currently loaded.

1.1 Databases

Databases are the main components in B3. A database is actually a set of entries, indexed bya unique key. Each entry has a type (e.g. article, book) and contains fields (e.g. title, authors,journal). The set of available fields depends on the entry type.

Two graphic components are directly linked with databases:

1. The Database Editor: list all entries, show a few description (Key, Authors, Year, Title).Allow sorting, search, edition of existing entry, addition or deletion of new entries, impor-tation from other databases or files.

2. The Entry Editor: appears when you double-click on an entry in the list. Here you can editeach field of an entry and modify its type.


Figure 1.2: A database with several entry, with one being edited.

The first internal frame from the left represents a database, with all entries in a table. It ispossible to sort alphabetically (a-z,0-9) by clicking on the header. To sort anti-alphabetically(z-a,9-0), click on the header while maintaining SHIFT down. The bottom panel is used todisplay search results.

The second internal frame is an Entry Editor, associated to the database. It is used to editand display each entry. It can be opened by double-clicking on an entry in the database, or ona search result. Le last window is part of the Entry Editor. It allow the edition of author/editornames.

B3 uses its own file format for storage, which can be seen as a XML version of the Bibtexformat. B3 proposes two versions of this format: ‘*.b3d’ files are text/xml files, and ‘*.b3z’and zipped xml files. The later format leads to smaller files, but writing and reading is slower.You can set the level of compression in the Configure panel.

1.2 Importing and file formats

Importing data means that you can add data from other formats into a B3 database. B3 canimport data in ‘*.b3d’ and ‘*.b3z’ format, but several additional formats are available. However,it is not possible to manage a database in one these formats, they are not fully implemented fornow and they could lead to a loss of data. A list of available formats for import is given in thefollowing table:

Format: Description: Implementation level:‘*.b3d’; ‘*.b3z’ B3 databases Full‘*.bib’ Bibtex file FullPubmed text Text output of Pubmed

database(deprecated, use XMLinstead)

Pubmed xml XML output of Pubmeddatabase

Full

RIS Reference Manager(c) format Articles only for now


EndNotes(c) export EndNotes(c) export format1 Articles only for now

It is also possible to scan recursively a directory for bibliographic data, and to fetch thePubmed database. whatever the importing procedure, the final step is the same: the entries aredisplayed in a BibView window.

1.2.1 The BibView window.

Once imported, entries appear in a special read-only component called BibView. This allowsyou to select which data you want to add to the database by selecting them. An integratedEntry Editor is available in right part of the panel.

Figure 1.3: The BibView component: a read-only database viewer and entry selector forimport.

1.2.2 Scanning a directory

This piece of utility try to import several files in a directory according to their extension. Thedialog allows yo to specify the file types you want to look for. You also have to specify thedirectory to check, and tell if you want to perform a recursive search. It is also possible toautomatically generate keys. Currently, the only available option is ’first author name + Year’.the ’Default’ option keeps the original key.

1 This is a plain text, tagged format, not the binary ‘.enl’ EndNotes file format! You have to export your file

in this format using the appropriate EndNotes filter.


Figure 1.4: Automatic scanning of directories for bibliographic data.

The results appear in a single BibView window.

1.2.3 Fetching Pubmed

It is possible to fetch Pubmed, by specifying a key, or by performing a search. Thesyntax used is the one specified by Pubmed (see http://www.nlm.nih.gov/bsd/pubmed_

tutorial/m1001.html for a complete tutorial).

Figure 1.5: Fetching Pubmed...

By default, only the 20 first entries are shown. It is possible to see the next 20 entries byclicking on the Next button, and/or to change the number of entries to display by setting thecorresponding spinner. Finally, the Resume button reset the counters to their initial state.

1.3 Using external applications

On several occasion, B3 may use external software installed on your system to display documents.In order to do so, you have to register them in the Options menu, Configre Mime-types sub-menu item. This will open a dialog box with possibility to add entries. There are two typesthat you will probably need:

OpenDocument

To be able to open OpenDocument (text) files. With open office or any OpenDoc-ument editor (can be openoffice.org3, oowriter, kwrite, abiword, depending on yoursystem and preference).

HTML To be able to display web pages. This is used by the Bookmarks menu for instance.This will typically be something like firefox or opera, but any other browser or webeditor can be used here.

Finally, you can add any document of your choice to bibliographic entry, and visualize themdirectly by providing a type. You just have to register the corresponding type in this dialog boxafter all. For instance, you will probably want to do something like


PDF With command acroread, evince, okular, xpdf or whatever.

Please note that the command you provide should be accessible, since it will be used verbatimin a system call. A secure option consists in providing the absolute path of the correspondingprogram on your system.

Chapter 2: Extended functions 6

2 Extended functions

2.1 The journal database

Articles entries contain a field named Journal. Journal may be displayed as fully named orabbreviated, for instance: Proceedings of the National Academy of Sciences of the USA orProc.Nat. Acad. Sci. or PNAS.

2.1.1 The Journal Dictionary

B3 includes a database with a set of journal names and corresponding abbreviations. You canaccess this database via the menu Journal -> Show Journal Dictionary Editor. You can editthis database providing you selected the corresponding check-box in the Options menu.

Figure 2.1: Browsing the journal database.

2.1.2 Checking journal names

When reading or importing a database, B3 can check if the journal fields are present in thedatabase and warn you if not. In order to do so, select the corresponding check-box in theOptions menu. When editing an entry, a pop-up window shows up to show you all possiblecompletions. This window can also be displayed via the Journals menu.

2.1.3 Switching between ’Full’ and ’Abbreviate’ modes

This is performed via the Options menu. Check the Use abbreviations check-box to switchto abbreviate mode. Check the Use dotted abbreviations check box to display dotted abbre-viations (ie Proc. Nat. Acad. Sci. instead of Proc Nat Acad Sci).

NB: This is only possible for entry whose journal is present in the dictionary.NB2: The selected mode will be used when processing the database with XSLT.


Figure 2.2: Automatic insertion of a journal name.

2.2 The author database

From version 2.50, I added the authors database functionality.

2.2.1 What is it for?

Managing an authors database may be useful to edit entries, you just have to choose the authorin a list instead of typing the whole name and stuff.

An author database may also be useful to store additional information on authors, like e-mailand address.

2.2.2 How does-it work?

A file named ‘AuthorsDb.xml’ is created in the user personal directory (‘~/.B3/authorDb.xml’).This XML file will contain all data of the authors database. You can move this file providingyou edit the configuration file accordingly. Since it’s not in B3’s home directory, it will not beoverwritten when installing a later version of B3 (different behavior from the Journal’s database).This file will automatically be created if you upgrade from a previous version of B3, please checkthe console for messages.

The authors database may be used in two ways:

1. By clicking on the ’Authors’ menu, and then the ’Show authors database’ item. This opensthe database request dialog, where you can check, edit, add or remove entries.


2. By editing an author field in any entry in your file. The author field as been updated, itis no longer a table. Double-clicking on an author brings a dialog box with several fields.From this dialog box, you can import authors from your database, or add any author bothto your entry and the database. Please note that the additional fields (’address’, ’e-mail’and ’notes’) are only for the database, they will not be stored in your bibliography file.

Figure 2.3: Importing authors and browsing the author database.

2.2.3 Adding entries to the author database

It’s possible to manually add entries by going to the ’Authors’ menu, and then clicking on the’Show authors database’ item. The ’Add’ button in the toolbar will bring a dialog box similarto the one for setting authors in an entry.

The other way is to automatically scan bibliography databases for authors. This is achievedby clicking on the corresponding item in the ’Authors’ menu. All authors in the current selectedbibliography will be added to the database.

Before adding an author to the base, B3 checks if any author with similar name are alreadypresent. If some are found, you’ll be asked to either add the author to the database or to dropthis one. An other possibility is to replace one of the existing entry by the new one. This isdone by selecting the entry you want to replace in the list and then clicking on the ’Replace’button. This functionality may be disabled by checking the corresponding item in the ’Authors’menu. Be careful that this may lead to duplicated entries!


Figure 2.4: Automatic scan for authors.

2.3 Searching a database (beta)

Version 2.90 includes a new general search tool that comes as a replacement for the old limited"author search" tool.

The search dialog is opened by going to the Search->Request menu item. A search requestfollows the general form:

FIELD_TYPE matching operator REGEXP

‘FIELD_TYPE’corresponds to the field to search (for now: "Author", "Year", "Title" or "Key-words").

‘REGEXP’ is a regular expression following Java regex format http://java.sun.com/j2se/

1.4.2/docs/api/java/util/regex/Pattern.html the java documentation for adetailed list of expressions allowed.

‘matching operator’is one of ’=’ (match) or ’ !=’ (do not match)

Several expression separated by a Boolean operator (’|’ OR or ’&’ AND) are allowed,and priority may be specified by parenthesis. Here is an example:

(AUTHOR=Kimura | AUTHOR=Tamura) & YEAR=19\d\d

Search for all entries with author "Kimura" or "Tamura" published in the XXth century.

Finally, the request dialog provides some shortcuts for typing the request.

2.4 Using style-sheets

B3 uses XSL style-sheet to process all entries in a database and write the result in several formatfor data exchange or pretty output. Each style-sheet may use only particular fields, however


the user can switch off any field he doesn’t want to be in the output using the ’Fields to export’panel. For now, B3 can write a Bibtex file for use with LaTeX or several display style in HTML:

‘Plain.b3s’Full sorted author names, index with numbers;

‘Abbreviate.b3s’The same with initials for authors’ first names;

‘Brieffing.b3s’List all fields in each entry + keys;

‘APA.b3s’ The American Psychological Association references format.

Figure 2.5: Using XSL style-sheet to export a bibliography. On the left: selection the fileand style-sheet. On the right: selecting the fields to export.

Chapter 3: Interacting with word processors 11

3 Interacting with word processors

3.1 Exporting to OpenOffice using a flat file

This section describes how to export a database in a flat text file. Each entry will be on aseparate line, with one field by column. Such file are often names CSV file (Coma SeparatedValue), because columns are separated by comas. Tabs or semi-columns are also frequently used.

Such Text/CSV file can be imported in OpenOffice(OOo) as a bibliography database. Itmay be convenient to export to OOo without using a database manager (DBM). However, flatfile are less powerful than DBMs. The next section will describe how to use a DBM to exportbibliographic data to OOo.

3.1.1 Export to a Text/CSV file.

3.1.1.1 The Database Configuration Dialog window

You first need to configure a few things. Go to the Options->Configure external database

I/O to access the Database Configuration Dialog. From here, you can set up the way you wantyour bibliography to be exported. These settings are for database export, of which CSV exportis a particular case.

Figure 3.1: Configure the database I/O first.

Fields

This table describes the correspondence between B3 entries fields (first column) andthe column name in the resulting table (second column). The third column is fordatabases only, and specifies the type of the column. It will be ignored for textexport.

Identifiers

Allows the creation a an additional column. Such a column is required for OOo. Itcontains a unique description of the entry, which will appear in your OOo document.It is possible to use the key of the entry, but other more “user-friendly” options maybe used:

Authors + year

the author list (last names), the year;


Short Authors + year

the same, but if there are more than 3 authors, use ’first author, et al.’notation;

Number the index of the entry in the list. Not very convenient, consider usingthe numbering option in OpenOffice instead.

Entry Types

Describes the correspondence between B3 entry types and the type that will appearin the “EntryType” column of your table.

Separators

Allows you to configure the way “Authors” and “Pages” fields will look in yourtable.

It is possible to save your settings to a XML file for latter re-use. As a consequence, it isalso possible to use a pre-defined configuration file. Two files for OOo export are downloadablefrom the website:

• http://kimura.univ-montp2.fr/~jdutheil/B3/Additional/OOo.dbc.xml, for export-ing to OOo using keys as identifiers.

• http://kimura.univ-montp2.fr/~jdutheil/B3/Additional/OOo.dbc_id.xml, forexporting to OOo using Authors description + Date as identifiers. For the rest of thissection, we will consider that your are using this configuration file.

3.1.1.2 Exporting a database

Got to the Export->Text/CSV menu, and choose the file where you want to export the data.The file must have the extension .txt or .csv to be recognized by OOo. An option dialog boxappears, letting you set the characters to be used for delimiting columns and so on. Usingtabulations to separate columns and double-quotes to delimit text is a reasonable choice.

3.1.2 Importing a Text/CSV file into OpenOffice.

This tutorial was done with OpenOffice 1.5.

OOo can import a database from a text file in CSV like format: a text file with columns.

3.1.2.1 Creating a new database

First of all, you must create a new bibliography database in OpenOffice. Click on the Data

Source menu item in the Tools menu. A dialog box then appears. Create a new source (Createnew source button, in the upper left corner). Set the general option as in figure Figure 3.2: setthe database type to text, set the database name and the directory where it can be found. Thenswitch to the “text” tab and set the format of you file: .csv extension for instance, and {tab}delimiter. The next panel allows you to select the table you want to use. One table shouldappear for each .csv file in the directory you selected in the “general” panel.


Figure 3.2: Choosing the database format.

3.1.2.2 Setting up the bibliography database

For now, you have imported your B3 data as a database in OpenOffice. The next step is to tellOpenOffice that this database is the one where you can find references.

To change the bibliography database, jump to the tools menu and select the ’bibliographydatabase’ menu item (the one just above ’data source’). A new Window appears:


Figure 3.3: Open Office bibliography database manager.

The database you see is the default database with references to OpenOffice books, or thelast one you used (in this case, you need not reading more of this tutorial ;-). You must changeto the new one you just created by clicking on the ’data source button’ (the last button in thetoolbar). Your database must appear in the list: just select it.

OpenOffice will now prompt you for the field assignation: answer ’yes’ to the question in thedialog box. Another window appears:

Figure 3.4: This dialog box allows you to set up the correspondence between B3 fields andthe table column names.

You can also display it with the column assignation button.

You may set something different, according to the fields you chose to export or else. Ifsome fields are set to ’nothing’, OpenOffice will prompt you again for column assignation. You


can answer ’no’ to the question, and it will work. Of course, you won’t be able to use thecorresponding field in the bibliography.

3.1.2.3 You’re done :-)

Here it ends! No you can insert reference as usual via the Insertion -> Index -> Bibliography

entry menu. Bibliography management in OpenOffice is beyond the scope of this tutorial, sogive a look at the OpenOffice help files for additional information.

3.2 Exporting to OpenOffice using MySQL

[This tutorial is contributed by Christian Wietholt.]

This tutorial is an attempt in helping people to export the reference database from B3into OpenOffice.org with the help of a MySQL database. As there are many distributions andOperating systems available, on which you can run B3 and MySQL, I am not able to cover allthe details. I assume that you installed MySQL successfully and you were able to log into theSQL manager with the commandline tool "mysql". Personally, I am using B3 and MySQL onDebian unstable, and I installed phpMyAdmin including a required web-server to administer theMySQL database. As this requires additional setup, I shall use the command line tool "mysql"that is distributed with the MySQL database.

First step in exporting your reference database to MySQL is to create a MySQL database.Log into your mySQL database manager using :

me@myDesktop:~\$ mysql --user me -p

Enter password: **********

Here I assume that you enabled password protection in your database manager, and alreadycreated a user with the required privileges to create, and alter a databases. Next you need tocreate a database with the following command :

mysql> create database myRefDB;

Query OK, 1 row affected (0.00 sec)

If you get the query OK response, everything should be fine, and you can exit your databasemanager by typing

exit

Now your database is created and waiting for you to fill it with data from B3. You can startB3 and load up bibliography database that you wish to export.

First step you need to do is load the correct configuration file for you database I/O seeFigure 3.5. This is essential for the bibliography database to work with OpenOffice.org. As theexpected reference database format changes with different OpenOffice.org version, you need tokeep this configuration updated. I am currently using OpenOffice 2.0.0.


Figure 3.5: Configure the database I/O first.

A recent I/O configuration file can be found at http://kimura.univ-montp2.fr/~jdutheil/B3/Additional

Load the downloaded XML file and close the dialog box:

Figure 3.6: Load the database I/O configuration file.

Now you can safely export your bibliography database to MySQL using the menu entryExport -> Export to SQL database.

A dialog will pop up to specify the MySQL database access information such as Driver,Domain, Port, Database, Username and Password. As a driver you need to choose MySQL, andset the other parameters appropriately. An example for accessing a database installed on youlocal machine is given in Figure 3.7. Then push the "Connect" button.


Figure 3.7: Export reference database to mySQL.

B3 will ask you for a table name in which the database will be stored in. I typically choose"biblio". This is the standard table name in OpenOffice. I experienced some problems duringmy initial tests with a different table name, so I suggest to stick with "biblio". If you areadventurous enough, you can try using different names. If this table does not exist, B3 willcreate it for you. Just click "OK" and if you need to create the table, click "Yes", and yourdata is exported.

Now it is time to start OpenOffice. First you need to open the database application. OOowill ask you what you want to do. You choose the option "Connect to existing database" asshown in Figure 3.8 and select of course "MySQL".

Figure 3.8: Connect to the mySQL database.

In the next wizard screen select the database driver you wish to use to connect to yourMySQL database. Here you should select the JDBC driver. In the following wizard screen youneed to input the connection details. In our case the appropriate configuration parameters areshown in the next figure:


Figure 3.9: Connect to the mySQL database parameter input.

In the next screen you need to input your user name and don’t forget to tick the passwordcheck-box if you have password protected access to your database manager. In the followingscreen, you need to make sure that the radio button "Yes, register the database for me" isselected. You can also choose to "Open the database for editing" to make sure that everythingworks as planned. See figure Ffigure 3.1 for details. Click on "Finish" and save your OpenOfficedatabase to a location of your choice. You can click on "tables" in OpenOffice Base to make surethat everything is working properly. OpenOffice should ask you for your password. In my case,accessing the table itself seems a little sluggish from OpenOffice Base, but the "BibliographyDatabase" dialog should work fine.

Ffigure 3.1: Connect to the mySQL database finished.

Now it is time to close OpenOffice Base and to open OpenOffice Writer. We choose the menuentry by going to Tools -> Bibliography Database.

Click on the tool bar entry "Data Source" and select the just registered database. Thename of the saved OpenOffice database will be available in the list menu. OpenOffice will askyou for your password, and your bibliography should appear in the spreadsheet field of the"Bibliography Database" dialog. As a next step I’d suggest to make sure that the columnarrangement is appropriately set. Just click on "Column Arrangement" in the tool bar of the"Bibliography Database" tool, and arrange the columns as shown in:


Figure 3.10: Make sure that the column Arrangement is set appropriately.

Now you can close the "Bibliography Database" dialog, and use the menu entry Insert ->

Indexes and Tables -> Bibliography Entry to insert your citations at the cursor position. Inthe pop-up dialog you should be able to choose the reference entry in the bibliography databasefrom a pull down menu. OpenOffice will place it at the cursor position after you pushed "Insert".If you want to create a bibliography table, select the menu entry Insert -> Indexes and Tables

-> Indexes and Tables.

Here choose the "Type" "Bibliography" and format the table to your desires, or journalrequirements.

Have fun with the great Open Source product.

3.3 Using LATEX

The insertion of citation in LaTeX document is facilitated by the LaTeX menu. This task maybe achieved in 3 steps:

1. Select one or several entries in a database, by clicking on the corresponding lines. Main-taining SHIFT key down allows to make a continuous selection, while maintaining CTRLkey down allows to make a multi-intervals selections.

2. Use the LaTeX menu (or the corresponding shortcut) to choose a LATEX command. For now,the standard \cite command and commands from the Natbib package are supported:

\cite CTRL+i\citet CTRL+t\citep CTRL+p\citealt CTRL+ALT+t\citealp CTRL+ALT+p\citeauthor CTRL+a\citeyear CTRL+y

The corresponding command is copied to clipboard.

3. Paste the content of the clipboard to your favorite LATEX editor (usually using CTRL+c).

3.4 Processing OpenDocument texts

[Please note that this functionality is still under testing and should be considered as “experi-mental”.]

From version 3.00, B3 can parse files in OpenDocument format. This principle is similar toEndNotes(C) RTF files parsing.


Basically, B3 looks for citations and check the references in a database. Then, it inserts thecorresponding formatted citation at the right place in the text, and compile the list of referenceaccording to a given style-sheet.

In order to do so, citations must follow a particular format, so that it be unambiguouslyrecognized by B3 during the parsing process. The syntax used is rather similar to the NatbibLaTeX package:

#B3citet SHIFT+t#B3citep SHIFT+p#B3citealt SHIFT+ALT+t#B3citealp SHIFT+ALT+p

It is possible to directly write these commands into your OpenDocument editor, or use theshortcuts or OpenDocument processor menu to automatically insert citations commands. Thiswill copy the command to the clipboard (See Section 3.3 [Using LaTeX], page 19).� �

3.4.1 Known issues and how to avoid them...

For the “display document” and “display bibliography” options to work, you need to registerthe corresponding mime-types in the options menu (See Section 1.3 [External Applications],page 4).

When working with document revisions, avoid to”break” the B3 reference tags, as it will notbe recognize. For the same reason, do not use formatting there (bold, italic, text decorationsand so one). To be on the safe side, always use the keyboard shortcuts to insert your references.

Index 21

Index

AAuthor database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

BB3 environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Bib View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

BibTex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

CCSV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

DDatabase Configuration Dialog . . . . . . . . . . . . . . . . . . . 11

Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Directory scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

EEndNotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Entry Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Exporting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

External . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

FFetching Pubmed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

File type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

HHTML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4, 9

IImporting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

JJournal abbreviation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Journal database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

KKey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

LLaTeX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

MMime-type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

MySQL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

OOpenDocument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

OpenOffice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11, 15

OpenOffice.org . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

PPDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Pubmed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

RReference Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Regular expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

RIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

SSearching a database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Stylesheets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

XXSLT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

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